I have not. I've had version control problems, where I've pulled the old file into a job instead of the current version, and I've navigated to the wrong folder to pull in the wrong version of the same named file though.
I'd suggest this:
Take the absolute latest version of the file and place it on the desktop.
Place the desktop file.
Then package the document to put the latest version of the linked graphic into the packaged folder.
Close and delete the original InDesign document. Work from the version in the packaged folder forevermore.
If you still have the old version of the file creeping back into the InDesign document, let us know. But I'll bet you a nickel that this will be the end of your problems.